Mass Effect: Loyalty
by IllusivePen
Summary: Shepard always tried to see the best in people and stay loyal to those who she thought deserved it. But then she died, and the whole world got turned upside-down before she was revived by Cerberus. Who will remain loyal now that she's with the evil pro-human organization? Who will see past the Cerberus badge on her uniform when they learn she's come back from the dead?
1. Chapter 1: Awakening

The last thing Shepard remembered, she was trying to rescue Joker from the Normandy SR-1. The Alliance flagship, the best in the fleet, had somehow managed to get destroyed in a single, surprise attack. It was just another routine mission, and it ended with Shepard gasping for air, then succumbing to the darkness. The Geth had not stopped her. Saren had not defeated her. The Reaper, Sovereign, could not prevail against her. But now, she was taken by a damaged space suit.

Murmurs, and then explosions and sirens. A strange voice called to her, beckoning her into action. As if Shepard had never left the battle on the Citadel, she jumped into the fray around her, hardly even noticing that her biotics seemed more precise and her aim almost effortless. Hardly noticing the Cerberus logos stamped on the walls of the facility where, apparently, mechs had gone haywire. All she could grasp was that she was alive, she had a gun, and someone needed her help.

"Shepard, you're alive!" said another unfamiliar voice. He called her over, introducing himself as Jacob, a former officer in the Alliance Navy. He shot a biotic blast toward some enemy mechs. "If Miranda has you up and running, things must be real bad."

"Miranda? What the hell is going on, and where am I?" Shepard thought the name sounded familiar, but couldn't place it. She popped out of cover and buried some bullets into the heads of two mechs across the room. When she dropped back down, Jacob checked to see that the coast was clear.

"Nice shooting, Commander. Good to know you haven't lost your edge. I know you've got questions, but things are bad here. We've gotta find Miranda and get the hell out of Dodge. We'll fill you in once we're safe, deal?"

Shepard nodded, "If that means you're going to help me stay alive, we have a deal."

They made it through a few rooms and found a stray scientist, and they managed to take down some security mechs with a biotic warp field. Shepard didn't even have time to analyze what was happening around her. Defense and survival were her highest priorities, and soon enough they found Miranda, who promptly shot their scientist companion.

"What the hell," Shepard exclaimed, pulling her gun up squarely at Miranda.

Jacob, clearly startled, put his hand on Shepard's gun. "Wait, Shepard, it's alright."

"Alright?! She just gunned down an innocent man!"

Miranda chimed in, and Shepard recognized her voice from the comms, the one who was telling her where to go and what to do. "Hardly innocent. He's the one who set the mechs on us."

Shepard hesitated, then slowly lowered her gun. Nothing about this served to abate her confusion. The strangers around her seemed like they knew her well enough, though Shepard didn't particularly feel like this "Miranda" liked her at all.

"Is someone going to fill me in, now that we've dealt with the pyrotechnics?"

"Let's get in the shuttle first," Miranda insisted, not waiting for them to follow before boarding.

"Shepard," Jacob started uneasily after they strapped in. "You've been dead for two years. Miranda here has been leading the team of scientists that rebuilt you." Jacob was a strong soldier, with powerful biotics. He seemed trustworthy. But the news he delivered seemed unreal. Shepard took a few long moments analyzing his face and Miranda's for some sign that they were joking. Failing that, she swallowed the lump which had been forming in her throat, her brows knit together.

"Shepard," Jacob continued, glancing at Miranda, "If I tell you who we work for, will you still trust us?"

"Jacob, I don't think-" Miranda started.

"She's going to find out sooner or later. She needs to know."

Shepard straightened in her seat and let out the breath she had been subconsciously holding. "What is it? I mean, you just told me I died and got resurrected. Are you sure you can still surprise me?" Her hands were held out in surrender.

Miranda sighed, continuing in her Aussie accent, "What Jacob's heart of gold is trying to say, Shepard, is that Cerberus rebuilt you. I was in charge of the team of scientists, and I answer directly to the Illusive Man himself." Miranda said this coolly, as if she hadn't just essentially told someone she had raised them from the dead like a freaking miracle-worker. She sounded bored.

"I… you… _what_?!" Shepard managed to squeeze out the question, leaning back in her chair and letting her arms go limp. As the cogs in her brain started to mesh together, she leaned forward again, her elbows on her knees. "Cerberus? The terrorist, pro-human organization? The one that experimented on both their own people and unknowing test subjects, sometimes leaving them to die from those experiments? Are we talking about the same Cerberus?"

"Yes," Jacob replied, defensively. "We've unfortunately had a bad rap in the last few years. But Cerberus is the only organization ready to help you fight the Reapers."

"...the Reapers." Shepard felt a chill run through her spine as she whispered it. "Two years have gone by, and _Cerberus_ is the only group that believes me? I hope to god you're wrong."

Miranda spoke up, crossing her arms and sounding annoyed, "You can discuss this with the Illusive Man yourself if you wish. He wants to speak with you when we land, which should be in a few minutes."

Shepard and Jacob shared an awkward glance, and the rest of the shuttle flight was silent, aside from the rattling of questions inside Shepard's head, and the threatening, mechanical hum of the engines.

* * *

Shepard was less than thrilled that this "meeting" with the Illusive Man was only through a vid-comm. The lack of face-to-face didn't help Shepard's automatic, though deserved, mistrust of Cerberus in general.

"Illusive Man, I presume?"

"Shepard. Good to see you made it out. I knew Miranda would get it done. We can't afford to lose you now."

"Look, I don't know what your angle is, but even if you did bring me back, I don't trust you."

"Your personal feelings aren't important right now. Humanity is on the brink of extinction, from a familiar foe."

Shepard grimaced knowingly, "Extinction? You mean the Reapers, don't you."

"Yes, the Reapers. We're at war, and nobody wants to admit it. But whole human colonies are disappearing, and we have reason to suspect the Reapers are behind it."

"Wait, you mean you haven't actually seen Reapers doing this?" Shepard's arms crossed in front of her as one suspecting eyebrow raised higher than the other.

"You've seen it yourself. Sovereign controlled Saren and the Geth. We think the Reapers are controlling whoever is abducting the human colonies. You took care of Sovereign, which is why we chose you. You are humanity's best chance for survival."

"But why go through the trouble of bringing me back? Why not talk to the council? Get help from the Alliance?" Shepard exhaled sharply, trying to stem the flow of questions trying to erupt through her mouth.

The Illusive Man exhaled a puff of smoke and tapped his cigarette. "Nobody is paying attention, because the attacks are random and happen in remote parts of the galaxy. Thousands of human colonists are disappearing, and while everyone else is turning a blind eye, Cerberus is doing something about it. We have reason to believe that they're targeting humanity because you killed one of them. You've got them scared."

Though he was starting to make sense, Shepard felt like he was still holding back information. His calm collectedness in the face of what he dubbed "human extinction" gave her an uncharacteristic urge to punch him in his cybernetic eyes. But she knew he had a point. She was probably Reaper Public Enemy Number One. She sighed and nodded. "All right. If what you say is true, that the Reapers are behind the disappearing colonies, I'll help. But I need proof." _And this doesn't stop with Humanity_ , she thought to herself.

"Good," Illusive Man said lightly. He took a sip of his drink, his face inscrutable. "We think you will be able to find what you're looking for at Freedom's Progress, the latest colony to be hit. Find out what happened, if there's a connection to the Reapers. Jacob and Miranda will take you in a shuttle and brief you. If you don't find what you're looking for, we can part ways. But I think you'll find that we have the same goals in this, Shepard. But don't take my word for it. Go ahead and find out for yourself."

Illusive Man's image fizzled out, and Shepard's face morphed into a grimmace. She still didn't feel like any of her bigger questions had been answered. She was still waiting for a practical joker to pop out behind a corner and say, "Gotcha!"

She stormed up the stairs and went to the armor station to prepare for the trip to Freedom's Progress. Miranda walked up. "We're ready to leave when you are, Commander." Shepard slammed a fist on the holo display and stopped, staring at the wall.

"I doubt I still have any rank, Miranda." Shepard drew in a deep breath and slowly let it out.

"Luckily for you," Miranda replied, "the Illusive Man has put us under your command. Just say the word, and we can go."

That bit of information caught her off guard. She straightened up and turned around, rearranging her thoughts. She took another deep breath. "We can go to Freedom's Progress, but I'm going to need some answers soon, or I think I might just go on a murderous rampage."

"I would expect you have a lot of questions," Jacob conceded. "Hopefully Freedom's Progress will clear some of them up."

"Hopefully." Shepard forcefully emptied out her lungs and shook her arms out, trying to loosen up. "Alright." She looked at the two Cerberus operatives, straight in the eyes. "If I'm in command, I need to know that I can trust you both to obey any order, is that clear?"

They both nodded, and Miranda replied, "You have my word. We both took an oath to keep you alive at all costs. So far, I'd say we've done well."

Shepard raised a curious brow at Miranda's tone, which was somewhat mocking. "If you have a problem with me, Miranda, I need to know before we land."

"It's nothing, Commander. We'll get the job done. What are your orders?"

With narrowed eyes, Shepard promptly filed Miranda under her "suspicious" file. "We'll go down and search for survivors first. Then we see if we can find out what happened and who took the colonists."

Both Jacob and Miranda saluted, then headed back to the shuttle.

Shepard exhaled sharply, then whispered to herself. "This is just the day that keeps on giving."


	2. Chapter 2: Freedom's Progress

Shepard gripped the railing on the side of the shuttle as they came in for a landing at Freedom's Progress. She didn't remember being afraid of heights before, but she thought that if she hadn't been wearing armor, her knuckles would have been white. Once they were on solid ground, the landing party jumped out of the door, and Shepard looked around. Once the engines died on the shuttle, Shepard could hear…. Nothing. No power generators, no distant conversations. But as soon as they turned one of the corners of a prefab building, some security mechs powered on, just like the ones that prompted her awakening at the Project Lazarus facility.

Shepard's heart raced and she pulled her gun out, hitting mech after mech, right between the optical sensors. Shepard took a deep breath once the mechs were taken care of. "Alright. If nobody's here, why are the security mechs active? Somebody had to have set them to attack anything that moves."

"Let's keep moving," Miranda suggested.

They went through another door, and Shepard drew her gun immediately upon seeing figures on the other side of the building. Those figures also drew their weapons, and Shepard immediately noted, by the exosuits and split-toe feet, that they were quarians. What were quarians doing here? Both sides stood pointing their weapons at each other as Shepard started to recognize one of the environment suits. Shepard tried to step closer when the figure dropped her shotgun. "Shepard?" She looked closer and immediately, fully recognized both the voice and the environmental suit around it. "Tali!" Shepard went to embrace her, but stopped when she saw Tali backing off and raising her shotgun again.

"Shepard, you… You're alive? And with _Cerberus_? What the hell?" Tali's voice was shaking, eyes barely glowing slits behind her almost opaque faceplate.

"Tali, I can explain…"

"What you can do is leave. Now," interrupted one of Tali's comrades.

Miranda stepped forward and put a presumptuous hand on her hip. "We have every right to be here, investigating a _human_ colony's disappearance. Why is there a group of quarians here? It looks awfully conspicuous."

"What we want to know is what Cerberus is doing here!" The other quarians were starting to gain more confidence in their positions. "You probably knew there was a quarian here on Pilgrimage, didn't you," the first soldier accused. "Probably came here to execute him, to cover up whatever happened here!"

Shepard slowly started pacing, trying to breathe deeply to catch her breath as the argument escalated on both sides. The noise was becoming unbearable and her fists clenched at her sides. "Everybody just SHUT THE HELL UP!" Everyone went silent, Shepard caught her breath, and she then continued with a forced calm. "Tali, we're not here for your pilgrim. Please trust me on this. Let's just keep going. We'll help take out any other mechs, and if the person you're looking for can help us figure out what happened here, then we can all get what we came for and leave. Deal?" Everyone glanced at everyone else, then slowly started nodding.

Tali spoke up carefully, but confidently. "Veetor should be further down by the cargo hold. We'll go around and meet you there."

The groups went their separate ways and managed to defeat a large contingent of security mechs near the cargo hold, but the quarians had tried to get there before Cerberus, and many were lost or wounded. Tali flat out refused Shepard's help, but insisted that she go find Veetor. "I have to help the wounded, Shepard. Go!"

And go she did. She went to the only locked door and bypassed it with her omni-tool. They found Veetor stammering in the dark, pouring over security footage from the abductions. Shepard looked over them as well, then placed a hand on Veetor's shoulder to get his attention.

Veetor jumped out of his chair. "What!? Wait… you're… You're not one of them… you're humans."

"You're safe now, Veetor. Just tell us what happened here."

Veetor brought up specific recorded events on the security recordings. Images of almost insectoid-humanoid creatures flooded the screens. The colonists were frozen in place before they even knew what was going on, and the creatures loaded them up into pods and carried them off to their ships. The barely comprehensible Veetor, obviously unstable and traumatized, concluded from the scans he had collected during the attack that these creatures were Collectors, and that they used "seeker swarms" to paralyze colonists. "Nobody escapes the swarms. They will come back for me," Veetor stammered, no longer sharing any useful information.

Tali finally made her way in, apparently done helping her squad. "Alright Shepard. You've got what you came for. Give me Veetor and we'll leave."

"No way," Miranda blurted, "The information he has is far too valuable. We need to take him with us."

"Seriously, Miranda?" Shepard turned on the woman, arms akimbo. She gestured toward the helpless quarian. "The information is all on his omni-tool. Even you should be smart enough to realize he can transfer that data to us." Miranda glared at Shepard, crossed her arms, and stepped back to lean against the wall.

"Thank you, Shepard," Tali said, sounding apologetic. "I…" she started, then turned to Veetor, tapping buttons on his omni-tool. "There, you should have the data, now." She looked at Shepard like she wanted to say more, but simply turned and left with Veetor.

Shepard sighed, looking through the data as her own omni-tool glowed around her forearm. "Well, that was fun."

"You alright, Shepard?" Jacob spoke up, carefully approaching her.

Shepard's omni-tool flickered off, and she started marching her way back toward the shuttle with her brows knit together. "I'm fine."

* * *

"Shepard, good work on Freedom's Progress," the holographic Illusive Man encouraged. "The omni-tool data proved quite thorough, and you confirmed that the Collectors are behind these attacks."

Shepard crossed her arms. "But is there any evidence that connects the Collectors to the Reapers, or are you just sending me out on a wild goose chase?"

"Normally, the Collectors only focus on small quantities of special-case individuals, trading them with technology. These large-scale abductions didn't start until after you and the human fleet destroyed Sovereign. There has to be a connection, and if anyone can figure it out, you can."

Shepard's hand pressed against her forehead as she tried to grasp any logical connection between the Collectors and the Reapers, but it just wasn't happening. But for now, Cerberus was the only way she was able to get any intel of any sort, so she had to play along. "Alright. Whatever the matter is, the fact remains that humans are under attack and nobody's doing anything about it. We won't wait. We'll take the fight to them. But I'll need a good team."

The Illusive Man tapped his cigarette ash. "I'll have Miranda forward some dossiers over to you. Some of the best soldiers, scientists, and mercenaries."

"I don't need mercs. I _had_ a good team when I went up against Saren."

"It's been two years, Shepard. Most of them have moved on. Changed loyalties."

That brought Shepard pause. Her voice lowered. "Like Tali. She seemed disgusted when she saw the Cerberus logo on my armor." Shepard had grown close to the quarian before, and desperately hoped that there was a good reason why Tali distanced herself. Something that Shepard wasn't at fault for. "What about Garrus Vakarian?"

"The Turian disappeared some time ago. Nobody's heard from him since a few months after your death."

"What about Kaidan Alenko? He's got to…" she stopped herself. She was really grasping at straws if she expected to recruit Alliance Alenko to a Cerberus team. The Illusive man all but confirmed this, reporting Kaidan's promotions and file classifications.

"Great." Shepard sighed, resigned to starting over, but determined to at least do some research of her own to find her old crew. "When do we head out?"

"As soon as you're ready. I suggest you go to Omega first. Mordin Solus, a brilliant salarian scientist, is there. He can come up with some way to counter the seeker swarms. Your ship is waiting for you in the docking area. And I think you'll like her pilot."

This whole time, The Illusive Man had tried to affirm that Shepard was in charge, but she was beginning to think the exact opposite. He was giving her "suggestions" but he still positioned himself as if he were an Admiral over her. The vid-comm fizzled out, and Shepard turned, gasping at the second familiar face she's seen in two years.

"Hey, Commander!" Joker said with a smile.

"Joker?!" Shepard flushed with relief, her smile wider than it had been since she woke up in the lab. She gave him a grateful hug, but just as suddenly scowled, backed up, and carefully punched his arm.

"OW!" Joker rubbed the spot. "What was that for?"

"For trying to go down with the damn ship, helmsman." Shepard actually took a step back and crossed her arms. She didn't expect to be angry at him, but as soon as she said it, it rooted into her mind, but she softened her face as she saw the guilt grow across his.

"Ah, geez. I'm sorry, Commander. I felt awful these past two years. If I had just…"

"It's OK, Joker," Shepard comforted, placing a gentle hand on the spot she punched. She didn't really want to be berated by guilt. "We're both here… and alive, by some miracle."

"Yeah… I know." They started working their way to the docking bay. "When I heard Cerberus was patching you up, I had to sign on. The Alliance wanted to shut up the whole Saren incident, and grounded me. Cerberus gave me a chance to fly again… and they gave me this…"

They had already made their way to the docking bay, and Shepard stopped dead in her tracks when she looked out the observation windows. Her heart leapt up to her throat and her jaw went slack. As if her old ship hadn't gotten blown up, but instead went to the salon to get a makeover, there she was: The Normandy SR2, glorious to behold, if marred by the Cerberus logo.

Shepard smiled and leaned on the railing in front of the windows. "She's beautiful."

Joker crossed his arms and nodded, "Yeah! Just wait 'till you get the full tour!"

Shepard moved to head toward the docking bay, but Joker stopped her. "Hey, Commander? I, uh… Thanks. Thanks for pulling my ass out of the Normandy. I… well, I'm glad you're back."

Shepard smirked at him. "Just don't lose this one, got it, Lieutenant?"

Joker seemed relieved that she didn't get sappy, and he saluted her. "Yes, ma'am!"


End file.
